SARS-CoV-2, the coronavirus responsible for the CoVID-19 syndrome, continues to be a major public health crisis worldwide. While the ongoing vaccination development and deployment efforts are a critical first line of defense, small-molecule therapeutics are needed to treat those who are infected and in desperate need of medical attention. Perhaps the most studied coronaviral target is the 3CL protease enzyme responsible for the proteolytic processing of the viral polyproteins pp1a and pp1ab which is essential for viral replication. We evaluated a series of five new compounds with four containing an (acyloxy)-methyl ketone reactive group including clinical candidate Pf-00835231 for their inhibitor potencies against SARS-CoV23CL protease. All five compounds exhibit remarkable potencies with Kivalues in the high picomolar to low nanomolar range against SARS-CoV-2. The X-ray structures of all five compounds were determined in complexes with SARS-CoV-2 3CLpro to between 1.4 Å and 1.6 Å resolution. All five compounds are observed to form a covalent bond with catalytic Cysteine 145 with four compounds forming adducts with the expected tetrahedral geometry. Compound 4 however, which contains an (acyloxy)-methyl ketone warhead, was found to form an adduct with bond geometries similar to an episulfonium cation. Despite possessing similar chemistry and scaffolds, inhibitor binding to the SARS-CoV-2 3CLpro induced a variety of subtle active site conformational differences, particularly in the S2/S4 separating strand and connecting strands.<div><br></div><div>Understanding substrate specificity in coronaviral main protease is essential for designing competitive inhibitors. While first principles are already established, including a Q/X cleavage-site (where X is either Alanine or Serine), differences exist between α, β, γand δ clades that are important for recognition, and ultimately inhibitor design. Covalent complexes of SARS-CoV-2 and avian infectious bronchitis virus (IBV) covalently bound, in trans, to the C-terminus of the same enzyme have been crystallized and modeled at 2.6 and 2.2 Å, respectively. The similarities and differences in their binding are described in chapter 6.<br></div><div><br></div><div>Middle-East Respiratory Syndrome Coronavirus is a re-emergent zoonotic pathogen with a 30% mortality rate in humans. The positive-sense single-stranded RNA genome is translated by the into polyproteins 1a (pp1a) and polyprotein 1ab (pp1ab). Pp1ab contains the constituents of the viral RNA-dependent RNA polymerase complex. These must be cleaved by 3CLpro, which is contained within this pair of polyproteins, before viral replication and transcription may occur. Attempts to drug this cysteine protease have proven difficult since competitive inhibitors activate the Wild-Type protease at low concentrations via a non-competitive binding mechanism. This mechanism is mediated by non-conserved residues in regions that are distal to the catalytic site. During the viral life-cycle these residues modulate recognition This study focuses on determining the identities of these residues and their effects on the dose-response curves of established competitive inhibitors of Coronaviral 3CLpro. It also explores how the residues in these regions synergize to effect intrinsic kinetic parameters of this family of enzymes including turnover (kcat) and dimer dissociation constant (KD). Additionally, a rapid-equilibrium kinetic model was developed to rationalize this unique phenomenon where competitive inhibitors cause significant activation of the enzyme’s activity.<br></div>

Conferencia online "Innovación y Propiedad Intelectual: retos en el momento actual". Con la participación del expositor Mario Matus, Director Adjunto de la Organización Mundial de la Propiedad Intelectual (OMPI) con sede en Ginebra.

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) was declared to be a pandemic and a public health emergency by the World Health Organization in March of 2020. Researchers and medical professionals worldwide have been working nonstop to better understand the disease process of COVID-19 in order to refine treatment protocols and create effective immunizations. Within the pandemic, children make up a unique patient population as they have shown to have similar but less severe clinical features when compared with infected adults. Most pediatric cases of COVID-19 have been reported as asymptomatic or mild with only 8 per 100,000 in the US requiring hospitalization between March 1-July 25, 2020, approximately 576 patients. The case presented is of a 4-year-old Caucasian female with an atypical presentation of a COVID-19-associated pneumonia, with a review of her presentation to the hospital, treatment plan, and discharge. The current frequency of pediatric cases of COVID-19 with severe disease is low, and thus, not fully understood. This case provides an example of successful diagnosis and in-patient treatment, and broadens the scope of severe disease potential from COVID-19 in the pediatric population.

Coronaviruses (CoVs) comprise a family of enveloped viruses that cause respiratory disease in humans, including CoV disease 2019 (COVID-19), caused by severe-acute respiratory syndrome CoV-2 (SARS-CoV-2). For CoV infection to occur, the CoV spike (S) protein must mediate fusion between the viral and host membranes. This entry process can also be repurposed during infection to promote cell-to-cell fusion, further contributing to viral spread. To trigger fusion, S must bind its cognate receptor and be cleaved by host proteases. Identifying cellular proteases capable of triggering CoV fusion is critical to understand CoV entry, tropism, and cell-cell spread, however the range of proteases capable of promoting CoV fusion has not been fully explored. Here, using fusion and entry assays, I provide evidence implicating matrix metalloproteinase-9 (MMP-9) as a fusion trigger for SARS-CoV-2 and HCoV-229E. Additionally, I show MMP-9 expression is upregulated during CoV infection, highlighting its potential relevance as a CoV triggering factor.

Thesis (Ph.D. in Microbiology) -- University of Colorado Denver, 2008. / Typescript. Includes bibliographical references (leaves 168-210). Free to UCD Anschutz Medical Campus. Online version available via ProQuest Digital Dissertations;

Master of Science in Biomedical Sciences / Department of Diagnostic Medicine/Pathobiology / Yunjeong Kim / Coronaviruses are pathogens that cause diverse diseases in humans and animals. The studies in this dissertation are focused on feline coronavirus (FCoV), ferret coronavirus (FRCoV) and mink coronavirus (MCoV). FCoV and FRCoV infections typically cause enteritis in cats and ferrets, respectively. However, a 100% fatal systemic disease called feline infectious peritonitis (FIP) can develop in some FCoV infected cats and a fatal systemic disease resembling FIP can develop in some FRCoV infected ferrets. MCoV causes enteritis which results in significant economic loss to mink farmers. No effective vaccine or treatment is available despite the increasing importance of these viral diseases. We have previously reported the synthesis of inhibitors against 3C-like protease (3CLpro) of FCoV and demonstrated the antiviral efficacy of a 3CLpro inhibitor for treating FIP. FRCoV and MCoV 3CLpro are closely related to FCoV 3CLpro. Therefore, we investigated the structure-function relationships of our 3CLpro inhibitors to identify the struc-tural requirements of inhibitors for FRCoV and MCoV. This is the first report of antiviral com-pounds against FRCoV and MCoV. We have previously conducted a field trial with a potent 3CLpro inhibitor, GC376, in cats with naturally occurring FIP. Comparison of the FCoV 3CLpro amino acid sequences from the pre- and post-treatment samples in one cat showed amino acid changes in 3CLpro. Hence, we generated recombinant 3CLpros carrying the amino acid changes and characterized the effects of these amino acid changes in FCoV 3CLpro on its susceptibility to GC376. We observed that these amino acid changes did not markedly affect the activity of GC376 in fluorescence resonance energy transfer (FRET) assay, explaining the absence of clinical drug resistance in this cat during the field trial.

Les différents génotypes de Coronavirus canins (CCoV-I/II) et félins (FCoV-I/II) sont phylogénétiquement proches, suggérant des transmissions inter-espèces entre chiens et chats. Lors d’analyses de séquences menées sur des chats infectés, des souches félines atypiques ont pu être mises en évidence, contenant un gène S de type FCoV-I, un gène N de type CCoV-I, ainsi que la présence du gène ORF3, spécifique à CCoV-I. Dans ces souches, le gène ORF3 est présent avec une ou deux délétions toujours identiques, conduisant à la synthèse de protéines tronquées gp3-Δ1 et gp3-Δ2. Les délétions de protéines accessoires étant déjà impliquées dans les transmissions inter-espèces, une étude de caractérisation de la protéine gp3 et de ses différentes formes a été menée. Les trois protéines s’oligomérisent de manière covalente et sont retenues dans le réticulum endoplasmique, en absence de signal spécifique de rétention. Les délétions influencent le niveau d’expression des protéines en cellules félines, où seule l’expression de gp3-Δ1 est visible, alors qu’elles conservent toutes une expression optimale en cellules canines. En l’absence de souches de Coronavirus cultivables en laboratoire contenant le gène ORF3, des cellules canines exprimant l’une des protéines gp3 ont été infectées par une souche CCoV-II. Dans ce modèle, les protéines gp3 ne modifient pas le cycle viral. Dans un contexte d’émergence de nouveaux Coronavirus, la compréhension des mécanismes moléculaires de changement d’hôte est cruciale et les Coronavirus félins et canins peuvent représenter un modèle d’étude utile. / The different genotypes of canine (CCoV-I/II) and feline (FCoV-I/II) Coronaviruses share a close phylogenetic relationship, suggesting inter-species transmissions between cats and dogs. Through sequence analyses of cat samples, atypical FCoV strains, harbouring an S gene related to FCoV-I, an N gene close to the CCoV-I cluster and the ORF3 gene, peculiar to CCoV-I, were discovered. This ORF3 gene was systematically truncated in feline samples, displaying either one or two identical deletions, leading to the translation of gp3-Δ1 and gp3-Δ2. As deletions in accessory proteins have already been involved in host-switch, studies of the different variants of gp3 were conducted. Results demonstrate that all proteins oligomerize through covalent bonds and are retained in the ER, without any specific retention signal. Deletions influence the expression level with a proper expression of the three proteins in canine cells, whereas only gp3-Δ1 expression is sustained in feline cells. As no isolates of Coronavirus harbouring the ORF3 gene exists, cells expressing the different gp3 proteins have been infected with a CCoV-II strain. In this model, the gp3 proteins do not influence the viral life cycle. In the light of emergence of new Coronaviruses, investigations on their molecular mechanisms during the host-switch are crucial and canine and feline Coronaviruses could represent a useful model.

published_or_final_version / abstract / Biological Sciences / Master / Master of Philosophy

published_or_final_version / Microbiology / Master / Master of Medical Sciences

An infectious cDNA clone of Vero cell adapted Beaudette strain of IBV was constructed using in vitro assembly of cDNA fragments. The entire genome of IBV was RT-PCR amplified into seven fragments, with each piece overlapping about 10 nucleotides. The fragments were ligated and transcribed to synthesize RNA, which was transfected into BHK-21 cells. These cells were then overlaid onto IBV susceptible Vero cells. After five days transfection, the virus was successfully rescued from the transfected cells. The cDNA clone from our laboratory strain has a five nucleotide insertion not present in the originally sequenced virus, resulting in total genome size of 27,613 nucleotides. The infectious cDNA clone was further manipulated to demonstrate its potential as a gene transfer vector, by replacing the ORF5a open reading frame with enhanced green fluorescent protein. The recombinant infectious cDNA clone was also successfully rescued after three days transfection of BHK-21 cells followed by co-culturing with Vero cells. This study showed that the 5a protein, whose function is not known, is not necessary for in vitro IBV replication. This study also showed that the 5a ORF is a good candidate for an insertion site of recombinant genes for the development of IBV infectious cDNA clone as a gene transfer vector.